--- imach/src/imach.c 2003/06/24 12:34:15 1.90
+++ imach/src/imach.c 2003/06/27 13:00:02 1.94
@@ -1,6 +1,25 @@
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $
+/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ Revision 1.94 2003/06/27 13:00:02 brouard
+ Just cleaning
+
+ Revision 1.93 2003/06/25 16:33:55 brouard
+ (Module): On windows (cygwin) function asctime_r doesn't
+ exist so I changed back to asctime which exists.
+ (Module): Version 0.96b
+
+ Revision 1.92 2003/06/25 16:30:45 brouard
+ (Module): On windows (cygwin) function asctime_r doesn't
+ exist so I changed back to asctime which exists.
+
+ Revision 1.91 2003/06/25 15:30:29 brouard
+ * imach.c (Repository): Duplicated warning errors corrected.
+ (Repository): Elapsed time after each iteration is now output. It
+ helps to forecast when convergence will be reached. Elapsed time
+ is stamped in powell. We created a new html file for the graphs
+ concerning matrix of covariance. It has extension -cov.htm.
+
Revision 1.90 2003/06/24 12:34:15 brouard
(Module): Some bugs corrected for windows. Also, when
mle=-1 a template is output in file "or"mypar.txt with the design
@@ -174,12 +193,12 @@
#define ODIRSEPARATOR '/'
#endif
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $ */
+/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $ */
/* $State: Exp $ */
-char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.90 $ $Date: 2003/06/24 12:34:15 $";
-int erreur; /* Error number */
+char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.94 $ $Date: 2003/06/27 13:00:02 $";
+int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
int npar=NPARMAX;
@@ -211,7 +230,7 @@ char fileresilk[FILENAMELENGTH]; /* File
FILE *ficresilk;
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;
-FILE *fichtm; /* Html File */
+FILE *fichtm, *fichtmcov; /* Html File */
FILE *ficreseij;
char filerese[FILENAMELENGTH];
FILE *ficresvij;
@@ -226,13 +245,21 @@ char command[FILENAMELENGTH];
int outcmd=0;
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-char lfileres[FILENAMELENGTH];
+
char filelog[FILENAMELENGTH]; /* Log file */
char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+
+struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+struct timezone tzp;
+extern int gettimeofday();
+struct tm tmg, tm, tmf, *gmtime(), *localtime();
+long time_value;
+extern long time();
+char strcurr[80], strfor[80];
#define NR_END 1
#define FREE_ARG char*
@@ -538,6 +565,41 @@ void free_ma3x(double ***m, long nrl, lo
free((FREE_ARG)(m+nrl-NR_END));
}
+/*************** function subdirf ***********/
+char *subdirf(char fileres[])
+{
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/"); /* Add to the right */
+ strcat(tmpout,fileres);
+ return tmpout;
+}
+
+/*************** function subdirf2 ***********/
+char *subdirf2(char fileres[], char *preop)
+{
+
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/");
+ strcat(tmpout,preop);
+ strcat(tmpout,fileres);
+ return tmpout;
+}
+
+/*************** function subdirf3 ***********/
+char *subdirf3(char fileres[], char *preop, char *preop2)
+{
+
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/");
+ strcat(tmpout,preop);
+ strcat(tmpout,preop2);
+ strcat(tmpout,fileres);
+ return tmpout;
+}
+
/***************** f1dim *************************/
extern int ncom;
extern double *pcom,*xicom;
@@ -713,6 +775,19 @@ void linmin(double p[], double xi[], int
free_vector(pcom,1,n);
}
+char *asc_diff_time(long time_sec, char ascdiff[])
+{
+ long sec_left, days, hours, minutes;
+ days = (time_sec) / (60*60*24);
+ sec_left = (time_sec) % (60*60*24);
+ hours = (sec_left) / (60*60) ;
+ sec_left = (sec_left) %(60*60);
+ minutes = (sec_left) /60;
+ sec_left = (sec_left) % (60);
+ sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ return ascdiff;
+}
+
/*************** powell ************************/
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
double (*func)(double []))
@@ -723,6 +798,8 @@ void powell(double p[], double **xi, int
double del,t,*pt,*ptt,*xit;
double fp,fptt;
double *xits;
+ int niterf, itmp;
+
pt=vector(1,n);
ptt=vector(1,n);
xit=vector(1,n);
@@ -733,9 +810,11 @@ void powell(double p[], double **xi, int
fp=(*fret);
ibig=0;
del=0.0;
- printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
- fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
- fprintf(ficrespow,"%d %.12f",*iter,*fret);
+ last_time=curr_time;
+ (void) gettimeofday(&curr_time,&tzp);
+ printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+ fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -743,7 +822,29 @@ void powell(double p[], double **xi, int
}
printf("\n");
fprintf(ficlog,"\n");
- fprintf(ficrespow,"\n");
+ fprintf(ficrespow,"\n");fflush(ficrespow);
+ if(*iter <=3){
+ tm = *localtime(&curr_time.tv_sec);
+ strcpy(strcurr,asctime(&tmf));
+/* asctime_r(&tm,strcurr); */
+ forecast_time=curr_time;
+ itmp = strlen(strcurr);
+ if(strcurr[itmp-1]=='\n')
+ strcurr[itmp-1]='\0';
+ printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+ fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+ for(niterf=10;niterf<=30;niterf+=10){
+ forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ tmf = *localtime(&forecast_time.tv_sec);
+/* asctime_r(&tmf,strfor); */
+ strcpy(strfor,asctime(&tmf));
+ itmp = strlen(strfor);
+ if(strfor[itmp-1]=='\n')
+ strfor[itmp-1]='\0';
+ printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+ fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+ }
+ }
for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);
@@ -1156,31 +1257,10 @@ double func( double *x)
oldm=newm;
} /* end mult */
- /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
- /* But now since version 0.9 we anticipate for bias and large stepm.
- * If stepm is larger than one month (smallest stepm) and if the exact delay
- * (in months) between two waves is not a multiple of stepm, we rounded to
- * the nearest (and in case of equal distance, to the lowest) interval but now
- * we keep into memory the bias bh[mi][i] and also the previous matrix product
- * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
- * probability in order to take into account the bias as a fraction of the way
- * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
- * -stepm/2 to stepm/2 .
- * For stepm=1 the results are the same as for previous versions of Imach.
- * For stepm > 1 the results are less biased than in previous versions.
- */
s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;
- /* bias is positive if real duration
- * is higher than the multiple of stepm and negative otherwise.
- */
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
- /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
- /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
- /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
- /*if(lli ==000.0)*/
- /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1207,30 +1287,10 @@ double func( double *x)
oldm=newm;
} /* end mult */
- /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
- /* But now since version 0.9 we anticipate for bias and large stepm.
- * If stepm is larger than one month (smallest stepm) and if the exact delay
- * (in months) between two waves is not a multiple of stepm, we rounded to
- * the nearest (and in case of equal distance, to the lowest) interval but now
- * we keep into memory the bias bh[mi][i] and also the previous matrix product
- * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
- * probability in order to take into account the bias as a fraction of the way
- * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
- * -stepm/2 to stepm/2 .
- * For stepm=1 the results are the same as for previous versions of Imach.
- * For stepm > 1 the results are less biased than in previous versions.
- */
s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;
- /* bias is positive if real duration
- * is higher than the multiple of stepm and negative otherwise.
- */
- /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
- /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
- /*if(lli ==000.0)*/
- /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1396,35 +1456,8 @@ double funcone( double *x)
return -l;
}
-char *subdirf(char fileres[])
-{
-
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/"); /* Add to the right */
- strcat(tmpout,fileres);
- return tmpout;
-}
-
-char *subdirf2(char fileres[], char *preop)
-{
-
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/");
- strcat(tmpout,preop);
- strcat(tmpout,fileres);
- return tmpout;
-}
-char *subdirf3(char fileres[], char *preop, char *preop2)
-{
-
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/");
- strcat(tmpout,preop);
- strcat(tmpout,preop2);
- strcat(tmpout,fileres);
- return tmpout;
-}
+/*************** function likelione ***********/
void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
{
/* This routine should help understanding what is done with
@@ -2036,6 +2069,7 @@ void concatwav(int wav[], int **dh, int
wav[i]=mi;
if(mi==0){
+ nbwarn++;
if(first==0){
printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;
@@ -2056,10 +2090,11 @@ void concatwav(int wav[], int **dh, int
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
if(j==0) j=1; /* Survives at least one month after exam */
else if(j<0){
+ nberr++;
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
- j=1; /* Careful Patch */
+ j=1; /* Temporary Dangerous patch */
printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
- printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
}
k=k+1;
@@ -2079,6 +2114,7 @@ void concatwav(int wav[], int **dh, int
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
if(j<0){
+ nberr++;
printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
}
@@ -2809,9 +2845,19 @@ void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n Computing and drawing one step probabilities with their confidence intervals
\n");
fprintf(fichtm,"\n");
- fprintf(fichtm,"\n Computing matrix of variance-covariance of step probabilities
\n");
- fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the pij, pkl to understand the covariance between two incidences. They are expressed in year-1 in order to be less dependent of stepm.
\n");
- fprintf(fichtm,"\n
We have drawn x'cov-1x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis.
When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.
\n");
+ fprintf(fichtm,"\n\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\nComputing matrix of variance-covariance of step probabilities
\n\
+ file %s
\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated\
+and drawn. It helps understanding how is the covariance between two incidences.\
+ They are expressed in year-1 in order to be less dependent of stepm.
\n");
+ fprintf(fichtmcov,"\n
Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+standard deviations wide on each axis.
\
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+ and made the appropriate rotation to look at the uncorrelated principal directions.
\
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n");
cov[1]=1;
tj=cptcoveff;
@@ -2993,13 +3039,13 @@ void varprob(char optionfilefiname[], do
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- fprintf(fichtm,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
+ fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
:\
%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtm,"\n
![](\"%s%d%1d%1d-%1d%1d.png\")
",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtm,"\n
Correlation at age %d (%.3f),",(int) age, c12);
+ fprintf(fichtmcov,"\n
",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n
Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
@@ -3008,7 +3054,7 @@ void varprob(char optionfilefiname[], do
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}else{
first=0;
- fprintf(fichtm," %d (%.3f),",(int) age, c12);
+ fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
@@ -3031,7 +3077,8 @@ void varprob(char optionfilefiname[], do
fclose(ficresprob);
fclose(ficresprobcov);
fclose(ficresprobcor);
- /* fclose(ficgp);*/
+ fflush(ficgp);
+ fflush(fichtmcov);
}
@@ -3674,9 +3721,14 @@ int fileappend(FILE *fichier, char *opti
fflush(fichier);
return (1);
}
+
+
+/**************** function prwizard **********************/
void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
{
+ /* Wizard to print covariance matrix template */
+
char ca[32], cb[32], cc[32];
int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
int numlinepar;
@@ -3794,6 +3846,7 @@ void prwizard(int ncovmodel, int nlstate
} /* end of prwizard */
+
/***********************************************/
/**************** Main Program *****************/
/***********************************************/
@@ -3857,15 +3910,10 @@ int main(int argc, char *argv[])
int lstra;
long total_usecs;
- struct timeval start_time, end_time, curr_time;
- struct timezone tzp;
- extern int gettimeofday();
- struct tm tmg, tm, *gmtime(), *localtime();
- long time_value;
- extern long time();
/* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
(void) gettimeofday(&start_time,&tzp);
+ curr_time=start_time;
tm = *localtime(&start_time.tv_sec);
tmg = *gmtime(&start_time.tv_sec);
strcpy(strstart,asctime(&tm));
@@ -3886,6 +3934,8 @@ int main(int argc, char *argv[])
* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
*/
+ nberr=0; /* Number of errors and warnings */
+ nbwarn=0;
getcwd(pathcd, size);
printf("\n%s\n%s",version,fullversion);
@@ -3934,9 +3984,11 @@ int main(int argc, char *argv[])
optionfilext=%s\n\
optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
- printf("Localtime (at start):%s",strstart);
- fprintf(ficlog,"Localtime (at start): %s",strstart);
+ printf("Local time (at start):%s",strstart);
+ fprintf(ficlog,"Local time (at start): %s",strstart);
fflush(ficlog);
+/* (void) gettimeofday(&curr_time,&tzp); */
+/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
/* */
strcpy(fileres,"r");
@@ -4328,11 +4380,13 @@ int main(int argc, char *argv[])
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+ nberr++;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+ nberr++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
@@ -4351,6 +4405,7 @@ int main(int argc, char *argv[])
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
else {
if ((int)andc[i]!=9999){
+ nbwarn++;
printf("Warning negative age at death: %ld line:%d\n",num[i],i);
fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
agev[m][i]=-1;
@@ -4387,6 +4442,7 @@ int main(int argc, char *argv[])
for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {
+ nberr++;
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
goto end;
@@ -4469,12 +4525,24 @@ int main(int argc, char *argv[])
/* fclose(ficgp);*/
/*--------- index.htm --------*/
- strcpy(optionfilehtm,optionfilefiname);
+ strcpy(optionfilehtm,optionfilefiname); /* Main html file */
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);
}
+ strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+ strcat(optionfilehtmcov,"-cov.htm");
+ if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
+ printf("Problem with %s \n",optionfilehtmcov), exit(0);
+ }
+ else{
+ fprintf(fichtmcov,"\nIMaCh Cov %s\n %s
%s \
+
\n\
+Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\
+ fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ }
+
fprintf(fichtm,"\nIMaCh %s\n %s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\
@@ -4485,18 +4553,14 @@ Title=%s
Datafile=%s Firstpass=%d La
- Log file of the run: %s
\n\
- Gnuplot file name: %s
\n\
- Date and time at start: %s\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
- model,fileres,fileres,\
+ fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
- /*fclose(fichtm);*/
fflush(fichtm);
strcpy(pathr,path);
strcat(pathr,optionfilefiname);
chdir(optionfilefiname); /* Move to directory named optionfile */
- strcpy(lfileres,fileres);
- strcat(lfileres,"/");
- strcat(lfileres,optionfilefiname);
/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */
@@ -5024,60 +5088,58 @@ ageminpar, agemax, s[lastpass][imx], age
fflush(ficgp);
- if(erreur >0){
- printf("End of Imach with error or warning %d\n",erreur);
- fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+ if((nberr >0) || (nbwarn>0)){
+ printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+ fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
}else{
- printf("End of Imach\n");
- fprintf(ficlog,"End of Imach\n");
+ printf("End of Imach\n");
+ fprintf(ficlog,"End of Imach\n");
}
printf("See log file on %s\n",filelog);
- fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
(void) gettimeofday(&end_time,&tzp);
tm = *localtime(&end_time.tv_sec);
tmg = *gmtime(&end_time.tv_sec);
strcpy(strtend,asctime(&tm));
- printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
- fprintf(ficlog,"Localtime at start %s\nLocal time at end %s",strstart, strtend);
- /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
-
- printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
- fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+ printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
+ fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
+ printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+
+ printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+ fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+ fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"
Local time at start %s
Local time at end %s
",strstart, strtend);
fclose(fichtm);
+ fclose(fichtmcov);
fclose(ficgp);
+ fclose(ficlog);
/*------ End -----------*/
- end:
-#ifdef windows
- /* chdir(pathcd);*/
-#endif
chdir(path);
- /*system("wgnuplot graph.plt");*/
- /*system("../gp37mgw/wgnuplot graph.plt");*/
- /*system("cd ../gp37mgw");*/
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);
printf("Starting graphs with: %s",plotcmd);fflush(stdout);
- system(plotcmd);
+ if((outcmd=system(plotcmd)) != 0){
+ printf(" Problem with gnuplot\n");
+ }
printf(" Wait...");
-
- /*#ifdef windows*/
while (z[0] != 'q') {
/* chdir(path); */
- printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+ printf("\nType e to edit output files, g to graph again and q for exiting: ");
scanf("%s",z);
- if (z[0] == 'c') system("./imach");
- else if (z[0] == 'e') system(optionfilehtm);
+/* if (z[0] == 'c') system("./imach"); */
+ if (z[0] == 'e') system(optionfilehtm);
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);
}
- /*#endif */
+ end:
+ while (z[0] != 'q') {
+ printf("\nType q for exiting: ");
+ scanf("%s",z);
+ }
}